I have tested my timers to voltages down to 2.5 volts and they still work properly, so a low (BEC) voltage would not account for a longer flight time than programmed. The flight time is determined by an internal clock what counts time based on a 50 Hz interrupt, and this is always within a percent or so of exact. A flight time malfunction is about the last thing I would expect, but I would appreciate further details on the timer and the equipment.